join program

[Bob]

Hello all,

I need to make deadzone coordinates for 25-base reads mm9 library. So far, I managed to get the unmappable regions using deadzone program. To merge these coordinates with unassembled regions downloaded off of USCS, the manual suggest using join.cpp.

It doesn't work for me. I don't even know what to expect and what the input output is, but I cannot find any documentation for the program.

Basically, here are my stepwise process according to the manual:

cat unassembled_mm9.bed unmappable-mm9-k25.bed > temp1.bed

sort -k1,1 -k2,2n temp1.bed > temp2.bed

But then I can simply cut the first 3 columns of temp2.bed and get the deadzones. 

So, what is the task of join.cpp? How can I run it? Is it

join temp2.bed > temp3.bed

(which does not produce any file) or there is another way to run it.

Thanks,

Robert